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- PDB-6cgl: X-ray crystal structure of Bacillus subtilis ribonucleotide reduc... -

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Basic information

Entry
Database: PDB / ID: 6cgl
TitleX-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound as-isolated (pH 4)
ComponentsRibonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / allostery / nucleotide metabolism / dAMP
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / ATP binding
Similarity search - Function
Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal ...Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Ribonucleoside-diphosphate reductase / Ribonucleoside-diphosphate reductase subunit alpha
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMaggiolo, A.O. / Boal, A.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: An endogenous dAMP ligand inBacillus subtilisclass Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP.
Authors: Parker, M.J. / Maggiolo, A.O. / Thomas, W.C. / Kim, A. / Meisburger, S.P. / Ando, N. / Boal, A.K. / Stubbe, J.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase
B: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,7269
Polymers161,5832
Non-polymers1,1437
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.646, 182.061, 155.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ribonucleoside-diphosphate reductase


Mass: 80791.469 Da / Num. of mol.: 2 / Fragment: \cf2 \cf0
Source method: isolated from a genetically manipulated source
Details: tag removed for crystallization / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3413, CFD21_09965 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A162Q3J9, UniProt: P50620*PLUS, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.39 % / Mosaicity: 0.339 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M citric acid (pH 4.0), 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2016
RadiationMonochromator: Si DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 37370 / % possible obs: 98.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.092 / Rrim(I) all: 0.224 / Χ2: 1.015 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.264.30.64216060.7230.3280.7240.92986.3
3.26-3.314.50.60117030.7810.2990.6730.94889.9
3.31-3.384.70.54517590.8360.2690.610.97293.1
3.38-3.454.70.51917920.8470.2570.5820.97396.1
3.45-3.525.10.52218660.8320.2490.5810.99298.2
3.52-3.65.20.44118740.8810.2110.4911.01499.2
3.6-3.695.80.45218760.8950.2050.4971.00499.6
3.69-3.796.10.40418930.9310.1780.4421.01699.7
3.79-3.916.10.3418580.9570.150.3721.03999.8
3.91-4.036.10.28719030.9620.1260.3141.02499.9
4.03-4.1860.24918900.9710.1110.2731.09499.7
4.18-4.345.90.21518900.9730.0970.2371.0599.9
4.34-4.5460.18818830.9760.0840.2061.059100
4.54-4.786.40.17819050.9830.0760.1941.053100
4.78-5.086.40.18219340.9820.0780.1981.031100
5.08-5.476.30.17618950.9850.0760.1920.98899.9
5.47-6.026.10.16919230.9810.0750.1860.966100
6.02-6.896.50.1619200.9870.0680.1740.943100
6.89-8.676.10.09819590.9930.0430.1070.87999.9
8.67-5060.06520410.9950.0280.0711.223100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PEM

1pem


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.819 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1700 4.8 %RANDOM
Rwork0.1972 ---
obs0.1998 33920 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.68 Å2 / Biso mean: 74.388 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---0.59 Å20 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10919 0 25 19 10963
Biso mean--86.81 29.85 -
Num. residues----1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210499
X-RAY DIFFRACTIONr_angle_refined_deg1.011.94815120
X-RAY DIFFRACTIONr_angle_other_deg0.845324195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83451334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99124.671563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.278152027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3131550
X-RAY DIFFRACTIONr_chiral_restr0.0570.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022654
LS refinement shellResolution: 3.201→3.284 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 95 -
Rwork0.314 1828 -
all-1923 -
obs--68.88 %

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